WO2006076102A3 - Fluorescent nucleoside analogs that mimic naturally occurring nucleosides - Google Patents

Fluorescent nucleoside analogs that mimic naturally occurring nucleosides Download PDF

Info

Publication number
WO2006076102A3
WO2006076102A3 PCT/US2005/044549 US2005044549W WO2006076102A3 WO 2006076102 A3 WO2006076102 A3 WO 2006076102A3 US 2005044549 W US2005044549 W US 2005044549W WO 2006076102 A3 WO2006076102 A3 WO 2006076102A3
Authority
WO
WIPO (PCT)
Prior art keywords
fluorescent
nucleoside analogs
naturally occurring
analogs
fluorescent nucleoside
Prior art date
Application number
PCT/US2005/044549
Other languages
French (fr)
Other versions
WO2006076102A2 (en
Inventor
Yitzhak Tor
Original Assignee
Univ California
Yitzhak Tor
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Univ California, Yitzhak Tor filed Critical Univ California
Priority to US11/792,968 priority Critical patent/US20080261823A1/en
Publication of WO2006076102A2 publication Critical patent/WO2006076102A2/en
Publication of WO2006076102A3 publication Critical patent/WO2006076102A3/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C07H19/067—Pyrimidine radicals with ribosyl as the saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/02—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings
    • C07D405/04—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D409/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having sulfur atoms as the only ring hetero atoms
    • C07D409/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having sulfur atoms as the only ring hetero atoms containing two hetero rings
    • C07D409/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having sulfur atoms as the only ring hetero atoms containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D413/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
    • C07D413/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings
    • C07D413/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
    • C07D417/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D491/00—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00
    • C07D491/02—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains two hetero rings
    • C07D491/04—Ortho-condensed systems
    • C07D491/044—Ortho-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring
    • C07D491/048—Ortho-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring the oxygen-containing ring being five-membered
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D491/00—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00
    • C07D491/12—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains three hetero rings
    • C07D491/14—Ortho-condensed systems
    • C07D491/147—Ortho-condensed systems the condensed system containing one ring with oxygen as ring hetero atom and two rings with nitrogen as ring hetero atom
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D495/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms
    • C07D495/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
    • C07D495/04—Ortho-condensed systems
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C07H19/073—Pyrimidine radicals with 2-deoxyribosyl as the saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Heterocyclic Carbon Compounds Containing A Hetero Ring Having Oxygen Or Sulfur (AREA)

Abstract

The present invention provides fluorescent nucleoside analogs with conjugated membered heterocycles, including furan and thiophene. The fluorescent nucleoside analogs maintain structural similarity to naturally occurring nucleoside bases, mimicking shape, size, hybridization, and recognition properties. Incorporation of the fluorescent cyclic compounds confers specific photophysical characteristics including a bathochromic (red) shift of the absorption spectrum to minimize absorption overlap with naturally occurring nucleoside bases, and a shift to the long emission wavelength in the visible range. The invention also provides for various methods of synthesizing the fluorescent nucleoside analogs and incorporating the fluorescent analogs in DNA, RNA, or oligomer synthesis. Further, methods of detecting the fluorescent nucleoside analogs in an oligonucleotide or oligomer are provided. The subject compounds are useful as probes in the study of the structure and dynamics of nucleic acids and their complexes with proteins.
PCT/US2005/044549 2004-12-10 2005-12-09 Fluorescent nucleoside analogs that mimic naturally occurring nucleosides WO2006076102A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
US11/792,968 US20080261823A1 (en) 2004-12-10 2005-12-09 Fluorescent Nucleoside Analogs That Mimic Naturally Occurring Nucleosides

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US63505204P 2004-12-10 2004-12-10
US60/635,052 2004-12-10

Publications (2)

Publication Number Publication Date
WO2006076102A2 WO2006076102A2 (en) 2006-07-20
WO2006076102A3 true WO2006076102A3 (en) 2007-05-31

Family

ID=36678068

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/044549 WO2006076102A2 (en) 2004-12-10 2005-12-09 Fluorescent nucleoside analogs that mimic naturally occurring nucleosides

Country Status (2)

Country Link
US (1) US20080261823A1 (en)
WO (1) WO2006076102A2 (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9371317B2 (en) 2013-02-19 2016-06-21 Senomyx, Inc. Sweet flavor modifier
US9382196B2 (en) 2008-07-31 2016-07-05 Senomyx, Inc. Processes and intermediates for making sweet taste enhancers

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9603848B2 (en) 2007-06-08 2017-03-28 Senomyx, Inc. Modulation of chemosensory receptors and ligands associated therewith
US7928111B2 (en) * 2007-06-08 2011-04-19 Senomyx, Inc. Compounds including substituted thienopyrimidinone derivatives as ligands for modulating chemosensory receptors
US8779118B2 (en) * 2010-01-11 2014-07-15 Isis Pharmaceuticals, Inc. Base modified bicyclic nucleosides and oligomeric compounds prepared therefrom
EP3593648B1 (en) 2012-08-06 2021-07-14 Firmenich Incorporated Sweet flavor modifier
MX2021001193A (en) 2018-08-07 2021-04-28 Firmenich Incorporated 5-substituted 4-amino-1h-benzo[c][1,2,6]thiadiazine 2,2-dioxides and formulations and uses thereof.

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5440040A (en) * 1988-06-10 1995-08-08 Medivir Ab Pyrimidine intermediates
US6479650B1 (en) * 1999-12-14 2002-11-12 Research Corporation Technologies, Inc. Fluorescent nucleoside analogs and combinatorial fluorophore arrays comprising same

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE69232816T2 (en) * 1991-11-26 2003-06-18 Isis Pharmaceuticals Inc INCREASED FORMATION OF TRIPLE AND DOUBLE HELICOS FROM OLIGOMERS WITH MODIFIED PYRIMIDINES

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5440040A (en) * 1988-06-10 1995-08-08 Medivir Ab Pyrimidine intermediates
US6479650B1 (en) * 1999-12-14 2002-11-12 Research Corporation Technologies, Inc. Fluorescent nucleoside analogs and combinatorial fluorophore arrays comprising same

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
EL-BARBARY A. ET AL.: "Synthesis of 5'-Amino- and 5'-Azido-2',5'-dideoxy Nucleosodes from Thieno[2,3-d]pyrimidine-2,4(1H,3H)-dione", MONATSHEFTE FUR CHEMIE, vol. 126, 1995, pages 593 - 600, XP008060014 *
GUTIEREZ A.J. ET AL.: "5-Heteroaryl-2'-deoxyuridine Analogs. Synthesis and Incorporation into High-Affinity Oligonucleotides", J. AM. CHEM. SOC., vol. 16, 1994, pages 5540 - 5544, XP003013139 *
OTTER B.A. ET AL.: "Pyrimidines. XII. A Propargyl Claisen Rearrangement in the Pyrimidine Series. Synthesis of Furo- and Pyrano[3,2-d]pyrimidines", J. ORG. CHEM., vol. 37, no. 18, 1972, pages 2858 - 2863, XP003013140 *

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9382196B2 (en) 2008-07-31 2016-07-05 Senomyx, Inc. Processes and intermediates for making sweet taste enhancers
US9371317B2 (en) 2013-02-19 2016-06-21 Senomyx, Inc. Sweet flavor modifier
US9475803B2 (en) 2013-02-19 2016-10-25 Senomyx, Inc. Sweet flavor modifier

Also Published As

Publication number Publication date
US20080261823A1 (en) 2008-10-23
WO2006076102A2 (en) 2006-07-20

Similar Documents

Publication Publication Date Title
WO2006076102A3 (en) Fluorescent nucleoside analogs that mimic naturally occurring nucleosides
CN101268188B (en) Novel artificial base pair and use thereof
CN109562376B (en) Single molecule/cluster DNA sequencing by synthesis based on fluorescence energy transfer
Chakraborty et al. Nucleic acid–based nanodevices in biological imaging
Holzhauser et al. DNA and RNA “traffic lights”: Synthetic wavelength-shifting fluorescent probes based on nucleic acid base substitutes for molecular imaging
ES2773438T3 (en) Modified nucleotide linkers
Park et al. Highly emissive deoxyguanosine analogue capable of direct visualization of B–Z transition
WO2005017181A3 (en) System for detecting polynucleotides
AU2021290387B2 (en) Labeled nucleotide compositions and methods for nucleic acid sequencing
WO2004072238A3 (en) Terminal-phosphate-labeled nucleotides with new linkers
WO2007020457A3 (en) Labelled modified guanine- containing nucleosides and nucleotides comprising a fluorophore attached to the base through a linking group comprising a polyethylene glycol spacing group and methods for their use
WO2006074162A3 (en) Primer generation rolling circle amplification
EP1959012A3 (en) Novel oligonucleotide compositions and probe sequences useful for detection and analysis of microRNAs and their target mRNAs
EA200800838A1 (en) MODULATION OF IMMUNE MULTIRATION PROPERTIES OF SHORT INTERFERRING RIBONUCLEIC ACID (SIPHK) BY MEANS OF NUCLEOTIDE MODIFICATION
CN108064264A (en) For the composition and method of allergen detection
WO2007106900A3 (en) Quantitative molecular probes
WO2007100711A3 (en) Methods and compositions for detecting polynucleotides
CN110118761A (en) A kind of signal enhancing type human serum ATP fluorescent optical sensor
WO2005112997A3 (en) Composition and method for introduction of dna directed or direct rna interference sequence into targeted cells and tissues
CN109406467A (en) Division aptamer sensor and its application for ATP detection
Molina et al. RNA-based boronate internucleosidic linkages: an entry into reversible templated ligation and loop formation
Sabale et al. Probing the competition between duplex and G-quadruplex/i-motif structures using a conformation-sensitive fluorescent nucleoside probe
Beerens et al. Role of the primer activation signal in tRNA annealing onto the HIV-1 genome studied by single-molecule FRET microscopy
Freyer et al. Binding of netropsin to several DNA constructs: Evidence for at least two different 1: 1 complexes formed from an–AATT-containing ds-DNA construct and a single minor groove binding ligand
WO2005014723A8 (en) Cyanin-type compounds having an alkynyl linker arm

Legal Events

Date Code Title Description
NENP Non-entry into the national phase

Ref country code: DE

121 Ep: the epo has been informed by wipo that ep was designated in this application
WWE Wipo information: entry into national phase

Ref document number: 11792968

Country of ref document: US

122 Ep: pct application non-entry in european phase

Ref document number: 05857063

Country of ref document: EP

Kind code of ref document: A2